For me, Markdown's issues relate to it's original purpose (which encapsulated use in emails) and it's use today (as a general long-form markup language).
I've found repeatedly that users dislike Markdown for the things that are hard to express in plain text (images, tables, links to some degree) and for surprising side effects of the syntax (in a hashtag age, headers appear too often and reduce readability, and the user misunderstands why).
What I would like to see is that Markdown is simplified further, and that some effort is made to find a better solution to links, images, etc.
I've found repeatedly that users dislike Markdown for the things that are hard to express in plain text (images, tables, links to some degree) and for surprising side effects of the syntax (in a hashtag age, headers appear too often and reduce readability, and the user misunderstands why).
What I would like to see is that Markdown is simplified further, and that some effort is made to find a better solution to links, images, etc.